What are the tools (which I can download and use) available for genotyping using low coverage whole genome re-sequencing data? Currently I can find MSG( Andolfatto et al 2011) and MPR(Xie et al 2010) are the two tools which uses HMM to genotype from a very low coverage resequencing ( < 1x coverage). Alternative tool is skim-based GBS(Bayer et al 2016) which basically use sliding window approach. It would be great if you can point out other tools available for this purpose? I am aware about IMPUTE2 and BEAGLE, but since they need a reference panel, its not really useful for me.
BTW: I am less interested in complexity reduced sequencing for genotyping( such as RAD-seq).
Thank you in advance